Gene Regulatory Network Modelling using Cuckoo Search and S-system

Gene regulatory network construction is a complex biological problem. Bio-inspired methods are well suited for solving biologically related optimization problems. In this paper, a new approach that combines the Ssystem and Cuckoo search for the reconstruction of gene regulatory network is introduced. All the processes related to genes are considered as chemical reactions. The popular rate law explains chemical reaction behaviour and participation of each molecule. Hence, S-system based on the rate law is considered as a suitable mathematical model for representing such biological reactions. In the proposed approach, genes are considered as the molecules for the reaction process. Gene reactions are considered reversible (mutually dependable) so that there can be cycles in the model. In order to test the effectiveness of the proposed approach it is implemented and tested on a five dimensional artificial data set and a real world data set of SOS DNA repair system of E.coli.. It is observed that the proposed approach converges faster than existing memetic algorithm and provides better reconstruction of the gene network. Keywords— Gene regulatory network, Bio-inspired methods, S-system, Cuckoo search, SOS DNA Repair system.

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